Nutritional grain quality is mainly influenced by the protein fraction content and grain protein content. Quantitative trait loci (QTL) mining for five traits, about 245 and 284 BC₃F₃ individual families of two introgression line (IL) populations were derived from Kongyu 131/Cypress (population-I) and Kongyu 131/Vary Tarva Osla (population-II), respectively. A genetic linkage map was developed using 127 simple sequence repeat (SSR) markers in population-I and 119 SSR markers in population-II. In total, 20 and 5 QTLs were detected in population-I and population-II, respectively. About twenty QTLs were mapped in population-I: five QTLs for albumin, seven QTLs for globulin, six QTLs for prolamin, one QTL for glutelin, and one QTL for grain protein content. In total, five QTLs were mapped in population-II: one QTL for albumin and four QTLs for grain protein content. Out of 25 QTLs, 19 QTLs exhibit co-localization with the previously reported QTLs. QTL-like qGPC7.3 was delineated for total protein content. This QTL was derived from population-I and was successfully validated in NILs (near-isogenic lines). The grain protein phenotype showed a significant variation between two NILs. This investigation serves as groundwork for additional cloning of nutritional quality-related genes in rice grains.

Grain size is a quantitative trait with a complex genetic mechanism, characterized by the combination of grain length (GL), grain width (GW), length to width ration (LWR), and grain thickness (GT). In this study, we conducted quantitative trait loci (QTL) analysis to investigate the genetic basis of grain size using BC₁F₂ and BC₁F_2:3 populations derived from two indica lines, Guangzhan 63-4S (GZ63-4S) and TGMS29 (core germplasm number W240). A total of twenty-four QTLs for grain size were identified, among which, three QTLs (qGW1, qGW7, and qGW12) controlling GL and two QTLs (qGW5 and qGL9) controlling GW were validated and subsequently fine mapped to regions ranging from 128 kb to 624 kb. Scanning electron microscopic (SEM) analysis and expression analysis revealed that qGW7 influences cell expansion, while qGL9 affects cell division. Conversely, qGW1, qGW5, and qGW12 promoted both cell division and expansion. Furthermore, negative correlations were observed between grain yield and quality for both qGW7 and qGW12. Nevertheless, qGW5 exhibited the potential to enhance quality without compromising yield. Importantly, we identified two promising QTLs, qGW1 and qGL9, which simultaneously improved both grain yield and quality. In summary, our results laid the foundation for cloning these five QTLs and provided valuable resources for breeding rice varieties with high yield and superior quality.